Open AccessVirtual Cell: computational tools for modeling in cell biology
Author(s) -
Resasco Diana C.,
Gao Fei,
Morgan Frank,
Novak Igor L.,
Schaff James C.,
Slepchenko Boris M.
Publication year - 2011
Publication title -
wiley interdisciplinary reviews: systems biology and medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.087
H-Index - 51
eISSN - 1939-005X
pISSN - 1939-5094
DOI - 10.1002/wsbm.165
Subject(s) - computational model , computational resource , computer science , computational simulation , virtual screening , modelling biological systems , biological system , systems biology , resource (disambiguation) , computational science , computational complexity theory , computational biology , simulation , algorithm , bioinformatics , biology , drug discovery , computer network
The Virtual Cell (VCell) is a general computational framework for modeling physicochemical and electrophysiological processes in living cells. Developed by the National Resource for Cell Analysis and Modeling at the University of Connecticut Health Center, it provides automated tools for simulating a wide range of cellular phenomena in space and time, both deterministically and stochastically. These computational tools allow one to couple electrophysiology and reaction kinetics with transport mechanisms, such as diffusion and directed transport, and map them onto spatial domains of various shapes, including irregular three‐dimensional geometries derived from experimental images. In this article, we review new robust computational tools recently deployed in VCell for treating spatially resolved models. WIREs Syst Biol Med 2012, 4:129–140. doi: 10.1002/wsbm.165 This article is categorized under: Models of Systems Properties and Processes > Cellular Models Analytical and Computational Methods > Computational Methods Models of Systems Properties and Processes > Mechanistic Models